Some tiny microbes are making a pretty big splash, and not just in the hot springs they call home in Yellowstone National Park. Recently, there was an interesting article published in Nature Microbiology about some amazing archaea, which are generally famous for inhabiting diverse extreme environments on the planet, including hot springs, hypersaline waters, and anoxic muds.
The first author of the paper, Luke McKay, wrote a succinct ‘Behind the Paper’ summary on the work reported in the study. In the article, the authors report the findings of a metagenomic analysis from samples collected from the Washburn Hot Springs in Yellowstone, which, as far as I can tell, looks like a beautiful place to hike. In 1870, an expedition led by General Washburn explored and mapped the land that eventually became Yellowstone National Park, and named one of the more famous geysers you might be familiar with, Old Faithful.
The Washburn hot spring with a pH of 6.4, is both sulfidic and anoxic and has plenty of methane, hydrogen and carbon dioxide (oh my!). The sediments are toasty, clocking in at 65-70 ºC. After the authors collected the sediment samples, they were put on dry ice, and stored frozen until DNA was extracted and sent for sequencing (on the Illumina HiSeq Platform at the Joint Genome Institute).
The authors describe two populations identified from the metagenome that fall within the ancient Korarchaeota. As a note, the term population here is referring to sequences from the metagenome that look to belong to one lineage. The sequences came from sediment, and therefore a whole microbial population made up of a bunch of cells representing multiple individuals from the same group belonging to a certain lineage that look to be very similar were sequenced together.
“An analysis of single-nucleotide variants showed that both genomes represented near-clonal environmental populations with low levels of strain heterogeneity.”
McKay et al., 2019
One population looks similar to a previously described bug (referred to as ‘Candidatus Korarchaeum cryptofilum OPF8′) while population numero dos the authors refer to as ‘Candidatus Methanodesulfokores washburnensis’. The candidate genus name of this second archaea (Methanodesulforkores), perhaps unsurprisingly, is quite descriptive since careful analyses reveal that this representative of the Korarchaeota harbors genes encoding enzymes for both anaerobic methane (mcr genes) AND dissimilatory sulfur (dsr genes) metabolisms.
The big deal here is that never before have the genes for both of these metabolisms been found in what possibly is one microbe. Additionally, previous studies have suggested that they likely are among the oldest of microbial metabolisms, suggesting that Candidatus Methanodesulfokores washburnensis could provide a glimpse into some of the first life on the planet.
“This organism contains genes that are necessary for methanogenesis from methanol and hydrogen, anaerobic oxidation of methane with sulfite and/or sulfite reduction with hydrogen.”
McKay et al., 2019
It should be noted, that’s not all that’s exciting in the world of archaea, simultaneously published (also in Nature Microbiology) is another article published by Borrel and colleagues (including McKay and Inskeep, also authors in the study discussed above). The article by Borrel et al.., represents an extensive analysis of thousands of metagenomes to better understand methanogenesis and methanotrophy. These processes are incredibly important to understand since they play an important part in global carbon cycling and ultimately have a role in climate change.
McKay and colleagues used their metagenome to delve into the world of microbial metabolism in the Washburn Hot Spring sediments, carefully picking apart the metabolic pathways identified by the genes sequenced. Decoding the hidden capacities encoded in these population genomes is one way to understand the diversity of the many fascinating, yet uncultured, microbes that have inhabited the earth for millions of years. The Greek root of Korarchaeota, is kore (young woman), an interesting choice for what looks to be quite an ancient phylum.
References
Borrel, G., Adam, P. S., McKay, L. J., Chen, L.-X., Sierra-García, I. N., Sieber, C. M. K., et al. (2019). Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology.
McKay, L. J., Dlakić, M., Fields, M. W., Delmont, T. O., Eren, A. M., Jay, Z. J., et al. (2019). Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nature Microbiology.
Rinehart, J.S., 1969. Old faithful geyser performance 1870 through 1966. Bulletin Volcanologique, 33(1), pp.153-163.